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Take this paper: https://dissem.in/p/131996/molecular-dynamics-simulations-of-electronalkali-cation-pairs-in-bulk-water which is correctly linked to HAL: https://hal.archives-ouvertes.fr/hal-00088127 …
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[Hou, Tingjun, Junmei Wang, Youyong Li, and Wei Wang. “Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Sim…
cramg updated
3 years ago
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Instead of implementing ES logic externally we prefer to use GROMACS to do this. This should reduce bugginess, instability and complexity.
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I just want to find a link to SSAGES.jl to add it to timestamps for [_Enhanced Sampling in Molecular Dynamics Simulations with Julia_ ](https://www.youtube.com/watch?v=a6sciHRP6m) and I landed here. T…
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Hello developer, first of all thank you for your work. I'd like to ask you two questions. First, whether it is possible to parmed the gromacs topology file (.top) into the charmm topology file (.psf),…
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[Maruca, Annalisa, Francesca Alessandra Ambrosio, Antonio Lupia, Isabella Romeo, Roberta Rocca, Federica Moraca, Carmine Talarico, et al. “Computer-Based Techniques for Lead Identification and Optimiz…
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Dear Said and colleagues,
I really like the approach of the ModSci ontology. Could you imagine to detail the physics/chemistry section and add terms like x-ray diffraction (XRD), quasi-elastic neut…
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is:issue is:open Hello! My name Zhukov Vladlen, I am Phd student. I tried to reproduced your supplementary. https://doi.org/10.1016/j.commatsci.2020.109951 But I came across a problem - the atoms in t…
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Hi
I was wondering if one can use groamcs-ramd to get binding events instead of unbinding. Is it possible to change the parameters in which the ligand approaches the binding site instead of getti…
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Part of charge development for carbohydrate molecular dynamics simulations requires an ensemble charge set. This charge set is built from PDB files which were extracted at regular intervals from a pr…